plot tracks for single cell RNAseq — importScSeqScore • trackViewer

Plot single cell RNAseq data as heatmap track for Seurat object.

importScSeqScore(
  object,
  files,
  samplenames,
  ...,
  txdb,
  gene,
  id,
  idents,
  gr,
  color,
  withCoverageTrack = TRUE,
  flag = scanBamFlag(isSecondaryAlignment = FALSE, isUnmappedQuery = FALSE,
    isNotPassingQualityControls = FALSE, isSupplementaryAlignment = FALSE)
)

Arguments

object: Seurat object.
files: bam file to be scanned.
samplenames: sample names for files.
...: parameters used by readGAlignmentsList or readGAlignments
txdb: TxDb object for gene model.
gene: Gene name to plot. (row value)
id: The id of gene used in txdb.
idents: indentity class to define the groups to plot. (column value)
gr: GRanges object to define the ploting region.
color: vector of colors used in heatmap.
withCoverageTrack: plot coverage track or not.
flag: An integer(2) vector used to filter reads based on their 'flag' entry.

Examples

if (FALSE) { # \dontrun{
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
test_file <- "https://github.com/10XGenomics/subset-bam/raw/master/test/test.bam"
trs <- importScSeqScore(files=test_file, 
                        txdb=TxDb.Hsapiens.UCSC.hg19.knownGene,
                        id="653635", gene = "WASH7P")
} # }